manifest:
  name: databio/lab
  version: 1.2.1
  imports:
  - bulker/biobase:default
  commands:
  - command: basemount
    docker_image: databio/basemount:0.25.2.3265
  - command: cellranger-atac
    docker_image: quay.io/cumulus/cellranger-atac:2.1.0
  - command: duc
    docker_image: databio/duc:1.4.6-lmdb
    docker_command: duc
    docker_args: -it
  - command: jq
    docker_image: linuxserver/yq
    entrypoint: jq
    docker_args: -i
  - command: R
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_22
    docker_command: R
    docker_args: -it
    description: You should add --volume=${HOME}/R/4.0:/usr/local/lib/R/host-site-library
      to tool_args
  - command: R3.6
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_10
    docker_command: R
    docker_args: -it
  - command: R4.0
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_11
    docker_command: R
    docker_args: -it
    description: You should add --volume=${HOME}/R/4.0:/usr/local/lib/R/host-site-library
      to tool_args
  - command: R4.0.3
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_12
    docker_command: R
    docker_args: -it
    description: You should add --volume=${HOME}/R/4.0:/usr/local/lib/R/host-site-library
      to tool_args
  - command: RC
    description: This image has all the latex stuff added in.
    docker_image: databio/bioconductor
    docker_command: R
    docker_args: -it
  - command: Rd
    description: R development release. To update, run docker pull bioconductor/bioconductor_docker:devel
    docker_image: bioconductor/bioconductor_docker:devel
    docker_command: R
    docker_args: -it
  - command: Rscript
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_22
    docker_command: Rscript
    docker_args: -it
  - command: Rscript3.6
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_10
    docker_command: Rscript
  - command: Rscript4.0
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_11
    docker_command: Rscript
    docker_args: -it
  - command: Rscript4.0.3
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_12
    docker_command: Rscript
    docker_args: -it
  - command: Rscriptd
    docker_image: bioconductor/bioconductor_docker:devel
    docker_command: Rscript
    docker_args: -it
  - command: stork
    docker_image: databio/stork
    docker_command: stork
  - command: xq
    docker_image: linuxserver/yq
    entrypoint: xq
    docker_args: -i
  - command: yq
    docker_image: linuxserver/yq
    entrypoint: yq
    docker_args: -i